Bio::Seq SequenceTrace
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Summary
Bio::Seq::SequenceTrace - Bioperl object packaging a sequence with its trace
Package variables
No package variables defined.
Included modules
Bio::PrimarySeq
Bio::PrimarySeqI
Bio::Seq::PrimaryQual
Bio::Seq::QualI
Inherit
Bio::Root::Root Bio::Seq::Quality Bio::Seq::TraceI
Synopsis
  # example code here
Description
This object stores a sequence with its trace.
Methods
newDescriptionCode
swq_obj
No description
Code
traceDescriptionCode
peak_indicesDescriptionCode
_reset_peak_indicesDescriptionCode
peak_index_atDescriptionCode
alphabetDescriptionCode
display_idDescriptionCode
accession_numberDescriptionCode
primary_idDescriptionCode
descDescriptionCode
idDescriptionCode
seqDescriptionCode
qualDescriptionCode
lengthDescriptionCode
qual_objDescriptionCode
seq_objDescriptionCode
_set_descriptorsDescriptionCode
subseqDescriptionCode
baseatDescriptionCode
subqualDescriptionCode
qualatDescriptionCode
sub_peak_indexDescriptionCode
sub_traceDescriptionCode
trace_lengthDescriptionCode
sub_trace_objectDescriptionCode
_synthesize_tracesDescriptionCode
_dump_tracesDescriptionCode
initialize_traces
No description
Code
trace_value_atDescriptionCode
_deprecated_get_scf_version_2_base_structure
No description
Code
_deprecated_get_scf_version_3_base_structure
No description
Code
accuraciesDescriptionCode
set_accuraciesDescriptionCode
scf_dumpDescriptionCode
_get_other_basesDescriptionCode
accuracy_atDescriptionCode
Methods description
new()code    nextTop
 Title   : new()
Usage : $st = Bio::Seq::SequenceTrace->new
( -swq => Bio::Seq::SequenceWithQuality,
-trace_a => \@trace_values_for_a_channel,
-trace_t => \@trace_values_for_t_channel,
-trace_g => \@trace_values_for_g_channel,
-trace_c => \@trace_values_for_c_channel,
-accuracy_a => \@a_accuracies,
-accuracy_t => \@t_accuracies,
-accuracy_g => \@g_accuracies,
-accuracy_c => \@c_accuracies,
-peak_indices => '0 5 10 15 20 25 30 35'
);
Function: Returns a new Bio::Seq::SequenceTrace object from basic
constructors.
Returns : a new Bio::Seq::SequenceTrace object
Arguments: I think that these are all describes in the usage above.
trace($base,\@new_values)codeprevnextTop
 Title   : trace($base,\@new_values)
Usage : @trace_Values = @{$obj->trace($base,\@new_values)};
Function: Returns the trace values as a reference to an array containing the
trace values. The individual elements of the trace array are not validated
and can be any numeric value.
Returns : A reference to an array.
Status :
Arguments: $base : which color channel would you like the trace values for?
- $base must be one of "A","T","G","C"
\@new_values : a reference to an array of values containing trace
data for this base
peak_indices($new_indices)codeprevnextTop
 Title   : peak_indices($new_indices)
Usage : $indices = $obj->peak_indices($new_indices);
Function: Return the trace index points for this object.
Returns : A scalar
Args : If used, the trace indices will be set to the provided value.
_reset_peak_indices()codeprevnextTop
 Title   : _rest_peak_indices()
Usage : $obj->_reset_peak_indices();
Function: Reset the peak indices.
Returns : Nothing.
Args : None.
Notes : When you create a sub_trace_object, the peak indices
will still be pointing to the apporpriate location _in the
original trace_. In order to fix this, the initial value must
be subtracted from each value here. ie. The first peak index
must be "1".
peak_index_at($position)codeprevnextTop
 Title   : peak_index_at($position)
Usage : $peak_index = $obj->peak_index_at($postition);
Function: Return the trace iindex point at this position
Returns : A scalar
Args : If used, the trace index at this position will be
set to the provided value.
alphabet()codeprevnextTop
 Title   : alphabet();
Usage : $molecule_type = $obj->alphabet();
Function: Get the molecule type from the PrimarySeq object.
Returns : What what PrimarySeq says the type of the sequence is.
Args : None.
display_id()codeprevnextTop
 Title   : display_id()
Usage : $id_string = $obj->display_id();
Function: Returns the display id, aka the common name of the Quality
object.
The semantics of this is that it is the most likely string to be
used as an identifier of the quality sequence, and likely to have
"human" readability. The id is equivalent to the ID field of the
GenBank/EMBL databanks and the id field of the Swissprot/sptrembl
database. In fasta format, the >(\S+) is presumed to be the id,
though some people overload the id to embed other information.
Bioperl does not use any embedded information in the ID field,
and people are encouraged to use other mechanisms (accession
field for example, or extending the sequence object) to solve
this. Notice that $seq->id() maps to this function, mainly for
legacy/convience issues.
This method sets the display_id for the Quality object.
Returns : A string
Args : If a scalar is provided, it is set as the new display_id for
the Quality object.
Status : Virtual
accession_number()codeprevnextTop
 Title   : accession_number()
Usage : $unique_biological_key = $obj->accession_number();
Function: Returns the unique biological id for a sequence, commonly
called the accession_number. For sequences from established
databases, the implementors should try to use the correct
accession number. Notice that primary_id() provides the unique id
for the implemetation, allowing multiple objects to have the same
accession number in a particular implementation. For sequences
with no accession number, this method should return "unknown".
This method sets the accession_number for the Quality
object.
Returns : A string (the value of accession_number)
Args : If a scalar is provided, it is set as the new accession_number
for the Quality object.
Status : Virtual
primary_id()codeprevnextTop
 Title   : primary_id()
Usage : $unique_implementation_key = $obj->primary_id();
Function: Returns the unique id for this object in this implementation.
This allows implementations to manage their own object ids in a
way the implementaiton can control clients can expect one id to
map to one object. For sequences with no accession number, this
method should return a stringified memory location.
This method sets the primary_id for the Quality
object.
Returns : A string. (the value of primary_id)
Args : If a scalar is provided, it is set as the new primary_id for
the Quality object.
desc()codeprevnextTop
 Title   : desc()
Usage : $qual->desc($newval); _or_
$description = $qual->desc();
Function: Get/set description text for this Quality object.
Returns : A string. (the value of desc)
Args : If a scalar is provided, it is set as the new desc for the
Quality object.
id()codeprevnextTop
 Title   : id()
Usage : $id = $qual->id();
Function: Return the ID of the quality. This should normally be (and
actually is in the implementation provided here) just a synonym
for display_id().
Returns : A string. (the value of id)
Args : If a scalar is provided, it is set as the new id for the
Quality object.
seqcodeprevnextTop
 Title   : seq()
Usage : $string = $obj->seq(); _or_
$obj->seq("atctatcatca");
Function: Returns the sequence that is contained in the imbedded in the
PrimarySeq object within the Quality object
Returns : A scalar (the seq() value for the imbedded PrimarySeq object.)
Args : If a scalar is provided, the Quality object will
attempt to set that as the sequence for the imbedded PrimarySeq
object. Otherwise, the value of seq() for the PrimarySeq object
is returned.
Notes : This is probably not a good idea because you then should call
length() to make sure that the sequence and quality are of the
same length. Even then, how can you make sure that this sequence
belongs with that quality? I provided this to give you rope to
hang yourself with. Tie it to a strong device and use a good
knot.
qual()codeprevnextTop
 Title   : qual()
Usage : @quality_values = @{$obj->qual()}; _or_
$obj->qual("10 10 20 40 50");
Function: Returns the quality as imbedded in the PrimaryQual object
within the Quality object.
Returns : A reference to an array containing the quality values in the
PrimaryQual object.
Args : If a scalar is provided, the Quality object will
attempt to set that as the quality for the imbedded PrimaryQual
object. Otherwise, the value of qual() for the PrimaryQual
object is returned.
Notes : This is probably not a good idea because you then should call
length() to make sure that the sequence and quality are of the
same length. Even then, how can you make sure that this sequence
belongs with that quality? I provided this to give you a strong
board with which to flagellate yourself.
length()codeprevnextTop
 Title   : length()
Usage : $length = $seqWqual->length();
Function: Get the length of the Quality sequence/quality.
Returns : Returns the length of the sequence and quality
Args : None.
qual_objcodeprevnextTop
 Title   : qual_obj($different_obj)
Usage : $qualobj = $seqWqual->qual_obj(); _or_
$qualobj = $seqWqual->qual_obj($ref_to_primaryqual_obj);
Function: Get the Qualilty object that is imbedded in the
Quality object or if a reference to a PrimaryQual object
is provided, set this as the PrimaryQual object imbedded in the
Quality object.
Returns : A reference to a Bio::Seq::Quality object.
Identical to seq_obj.
seq_objcodeprevnextTop
 Title   : seq_obj()
Usage : $seqobj = $seqWqual->seq_obj(); _or_
$seqobj = $seqWqual->seq_obj($ref_to_primary_seq_obj);
Function: Get the PrimarySeq object that is imbedded in the
Quality object or if a reference to a PrimarySeq object is
provided, set this as the PrimarySeq object imbedded in the
Quality object.
Returns : A reference to a Bio::PrimarySeq object.
_set_descriptorscodeprevnextTop
 Title   : _set_descriptors()
Usage : $seqWqual->_qual_obj($qual,$seq,$id,$acc,$pid,$desc,$given_id,
$alphabet);
Function: Set the descriptors for the Quality object. Try to
match the descriptors in the PrimarySeq object and in the
PrimaryQual object if descriptors were not provided with
construction.
Returns : Nothing.
Args : $qual,$seq,$id,$acc,$pid,$desc,$given_id,$alphabet as found
in the new() method.
Notes : Really only intended to be called by the new() method. If
you want to invoke a similar function try
set_common_descriptors().
subseq($start,$end)codeprevnextTop
 Title   : subseq($start,$end)
Usage : $subsequence = $obj->subseq($start,$end);
Function: Returns the subseq from start to end, where the first base
is 1 and the number is inclusive, ie 1-2 are the first two
bases of the sequence.
Returns : A string.
Args : Two positions.
baseat($position)codeprevnextTop
 Title   : baseat($position)
Usage : $base_at_position_6 = $obj->baseat("6");
Function: Returns a single base at the given position, where the first
base is 1 and the number is inclusive, ie 1-2 are the first two
bases of the sequence.
Returns : A scalar.
Args : A position.
subqual($start,$end)codeprevnextTop
 Title   : subqual($start,$end)
Usage : @qualities = @{$obj->subqual(10,20);
Function: returns the quality values from $start to $end, where the
first value is 1 and the number is inclusive, ie 1-2 are the
first two bases of the sequence. Start cannot be larger than
end but can be equal.
Returns : A reference to an array.
Args : a start position and an end position
qualat($position)codeprevnextTop
 Title   : qualat($position)
Usage : $quality = $obj->qualat(10);
Function: Return the quality value at the given location, where the
first value is 1 and the number is inclusive, ie 1-2 are the
first two bases of the sequence. Start cannot be larger than
end but can be equal.
Returns : A scalar.
Args : A position.
sub_peak_index($start,$end)codeprevnextTop
 Title   : sub_peak_index($start,$end)
Usage : @peak_indices = @{$obj->sub_peak_index(10,20);
Function: returns the trace index values from $start to $end, where the
first value is 1 and the number is inclusive, ie 1-2 are the
first two trace indices for this channel.
Returns : A reference to an array.
Args : a start position and an end position
sub_trace($start,$end)codeprevnextTop
 Title   : sub_trace($base_channel,$start,$end)
Usage : @trace_values = @{$obj->sub_trace('a',10,20)};
Function: returns the trace values from $start to $end, where the
first value is 1 and the number is inclusive, ie 1-2 are the
first two bases of the sequence. Start cannot be larger than
end but can be e_peak_index.
Returns : A reference to an array.
Args : a start position and an end position
trace_length()codeprevnextTop
 Title   : trace_length()
Usage : $trace_length = $obj->trace_length();
Function: Return the length of the trace if all four traces (atgc)
are the same. Otherwise, throw an error.
Returns : A scalar.
Args : none
sub_trace_object($start,$end)codeprevnextTop
 Title   : sub_trace_object($start,$end)
Usage : $smaller_object = $object->sub_trace_object('1','100');
Function: Get a subset of the sequence, its quality, and its trace.
Returns : A reference to a Bio::Seq::SequenceTrace object
Args : a start position and an end position
Notes :
- the start and end position refer to the positions of _bases_.
- for example, to get a sub SequenceTrace for bases 5-10,
use this routine.
- you will get the bases, qualities, and the trace values
- you can then use this object to synthesize a new scf
using seqIO::scf.
_synthesize_traces()codeprevnextTop
 Title   : _synthesize_traces()
Usage : $obj->_synthesize_traces();
Function: Synthesize false traces for this object.
Returns : Nothing.
Args : None.
Notes : This method is intended to be invoked when this
object is created with a SWQ object- that is to say that
there is a sequence and a set of qualities but there was
no actual trace data.
_dump_traces($transformed)codeprevnextTop
 Title   : _dump_traces("transformed")
Usage : &_dump_traces($ra,$rc,$rg,$rt);
Function: Used in debugging. Prints all traces one beside each other.
Returns : Nothing.
Args : References to the arrays containing the traces for A,C,G,T.
Notes : Beats using dumpValue, I'll tell ya. Much better then using
join' ' too.
- if a scalar is included as an argument (any scalar), this
procedure will dump the _delta'd trace. If you don't know what
that means you should not be using this.
trace_value_at($channel,$position)codeprevnextTop
 Title   : trace_value_at($channel,$position)
Usage : $value = $trace_object->trace_value_at($channel,$position);
Function: What is the value of the trace for this base at this position?
Returns : A scalar represnting the trace value here.
Args : a base channel (a,t,g,c)
a position ( < $trace_object->trace_length() )
accuracies($channel,$position)codeprevnextTop
 Title   : trace_value_at($channel,$position)
Usage : $value = $trace_object->trace_value_at($channel,$position);
Function: What is the value of the trace for this base at this position?
Returns : A scalar representing the trace value here.
Args : a base channel (a,t,g,c)
a position ( < $trace_object->trace_length() )
set_accuracies()codeprevnextTop
 Title   : set_sccuracies()
Usage : $trace_object->set_accuracies();
Function: Take a sequence's quality and synthesize proper scf-style
base accuracies that can then be accessed with
accuracies("a") or something like it.
Returns : Nothing.
Args : None.
scf_dump()codeprevnextTop
 Title   : scf_dump()
Usage : $trace_object->scf_dump();
Function: Prints out the contents of the structures representing
the SequenceTrace in a manner similar to io_lib's scf_dump.
Returns : Nothing. Prints out the contents of the structures
used to represent the sequence and its trace.
Args : None.
Notes : Used in debugging, obviously.
_get_other_bases($this_base)codeprevnextTop
 Title   : _get_other_bases($this_base)
Usage : $other_bases = $trace_object->_get_other_bases($this_base);
Function: A utility routine to return bases other then the one provided.
I was doing this over and over so I put it here.
Returns : Three of a,t,g and c.
Args : A base (atgc)
Notes : $obj->_get_other_bases("a") returns "tgc"
accuracy_at($base,$position)codeprevnextTop
 Title   : accuracy_at($base,$position)
Usage : $accuracy = $trace_object->accuracy_at($base,$position);
Function:
Returns : Returns the accuracy of finding $base at $position.
Args : 1. a base channel (atgc) 2. a value to _set_ the accuracy
Notes : $obj->_get_other_bases("a") returns "tgc"
Methods code
newdescriptionprevnextTop
sub new {
    my ($class, @args) = @_;
    my $self = $class->SUPER::new(@args);
	# default: turn OFF the warnings
$self->{supress_warnings} = 1; my($swq,$peak_indices,$trace_a,$trace_t, $trace_g,$trace_c,$acc_a,$acc_t,$acc_g,$acc_c) = $self->_rearrange([qw( SWQ PEAK_INDICES TRACE_A TRACE_T TRACE_G TRACE_C ACCURACY_A ACCURACY_T ACCURACY_G ACCURACY_C )], @args); # first, deal with the sequence and quality information
if ($swq && ref($swq) eq "Bio::Seq::Quality") { $self->{swq} = $swq; } else { $self->throw("A Bio::Seq::SequenceTrace object must be created with a Bio::Seq::Quality object. You provided this type of object: " .ref($swq)); } if (!$acc_a) { # this means that you probably did not provide traces and accuracies
# and that they need to be synthesized
$self->set_accuracies(); } else { $self->accuracies('a',$acc_a); $self->accuracies('t',$acc_t); $self->accuracies('g',$acc_g); $self->accuracies('c',$acc_c); } if (!$trace_a) { $self->_synthesize_traces(); } else { $self->trace('a',$trace_a); $self->trace('t',$trace_t); $self->trace('g',$trace_g); $self->trace('c',$trace_c); $self->peak_indices($peak_indices); } $self->id($self->seq_obj->id); return $self;
}
swq_objdescriptionprevnextTop
sub swq_obj {
     my $self = shift;
     $self->warn('swq_obj() is deprecated: use seq_obj()');
     return $self->{swq};
}
tracedescriptionprevnextTop
sub trace {
   my ($self,$base_channel,$values) = @_;
     if (!$base_channel) {
          $self->throw('You must provide a valid base channel (atgc) to use trace()');
     }
     $base_channel =~ tr/A-Z/a-z/;
     if ($base_channel !~ /[acgt]/) {
          $self->throw('You must provide a valid base channel (atgc) to use trace()');
     }
     if ($values) {
             if (ref($values) eq "ARRAY") {
                  $self->{trace}->{$base_channel} = $values;
             }
             else {
                    my @trace = split(' ',$values);
                  $self->{trace}->{$base_channel} =\@ trace;
             }
     }
     if ($self->{trace}->{$base_channel}) {
          return $self->{trace}->{$base_channel};
     }
     else {
          return;
     }
}
peak_indicesdescriptionprevnextTop
sub peak_indices {
   my ($self,$peak_indices)= @_;
     if ($peak_indices) {
          if (ref($peak_indices) eq "ARRAY") {
               $self->{peak_indices} = $peak_indices;
          }
          else {
               my @indices = split(' ',$peak_indices);
               $self->{peak_indices} =\@ indices;
         } 
     }
     if (!$self->{peak_indices}) {
          my @temp = ();
          $self->{peak_indices} =\@ temp;
     }
     return $self->{peak_indices};
}
_reset_peak_indicesdescriptionprevnextTop
sub _reset_peak_indices {
   my $self = shift;
     my $length = $self->length();
     my $subtractive = $self->peak_index_at(1);
     my ($original,$new);
     $self->peak_index_at(1,"null");
     for (my $counter=2; $counter<= $length; $counter++) {
          my $original = $self->peak_index_at($counter);
          $new = $original - $subtractive;
          $self->peak_index_at($counter,$new);
     }
     return;
}
peak_index_atdescriptionprevnextTop
sub peak_index_at {
   my ($self,$position,$value)= @_;
   if ($value) {
          if ($value eq "null") {
               $self->peak_indices->[$position-1] = "0";
          }
          else {
               $self->peak_indices->[$position-1] = $value;
          }
   }
    return $self->peak_indices()->[$position-1];
}
alphabetdescriptionprevnextTop
sub alphabet {
	my $self = shift;
	return $self->{swq}->alphabet;
}
display_iddescriptionprevnextTop
sub display_id {
   my ($self,$value) = @_;
   if( defined $value) {
      $self->{swq}->display_id($value);
    }
    return $self->{swq}->display_id();
}
accession_numberdescriptionprevnextTop
sub accession_number {
    my( $self, $acc ) = @_;
    if (defined $acc) {
        $self->{swq}->accession_number($acc);
    } else {
        $acc = $self->{swq}->accession_number();
        $acc = 'unknown' unless defined $acc;
    }
    return $acc;
}
primary_iddescriptionprevnextTop
sub primary_id {
   my ($self,$value) = @_;
   if ($value) {
      $self->{swq}->primary_id($value);
    }
   return $self->{swq}->primary_id();
}
descdescriptionprevnextTop
sub desc {
	# a mechanism to set the desc for the Quality object.
# probably will be used most often by set_common_features()
my ($self,$value) = @_; if( defined $value) { $self->{swq}->desc($value); } return $self->{swq}->desc();
}
iddescriptionprevnextTop
sub id {
   my ($self,$value) = @_;
   if (!$self) { $self->throw("no value for self in $value"); }
   if( defined $value ) {
       $self->{swq}->display_id($value);
   }
   return $self->{swq}->display_id();
}
seqdescriptionprevnextTop
sub seq {
	my ($self,$value) = @_;
	if( defined $value) {
		$self->{swq}->seq($value);
	}
	return $self->{swq}->seq();
}
qualdescriptionprevnextTop
sub qual {
	my ($self,$value) = @_;

	if( defined $value) {
		$self->{swq}->qual($value);
	}
	return $self->{swq}->qual();
}
lengthdescriptionprevnextTop
sub length {
    my $self = shift;
    return $self->seq_obj->length;
}
qual_objdescriptionprevnextTop
sub qual_obj {
    my ($self,$value) = @_;
#    return $self->{swq}->qual_obj($value);
return $self->{swq};
}
seq_objdescriptionprevnextTop
sub seq_obj {
    my ($self,$value) = @_;
    return $self->{swq};
}
_set_descriptorsdescriptionprevnextTop
sub _set_descriptors {
    my ($self,$qual,$seq,$id,$acc,$pid,$desc,$given_id,$alphabet) = @_;
    $self->{swq}->_seq_descriptors($qual,$seq,$id,$acc,$pid,
				   $desc,$given_id,$alphabet);
}
subseqdescriptionprevnextTop
sub subseq {
    my ($self,@args) = @_;
    # does a single value work?
return $self->{swq}->subseq(@args);
}
baseatdescriptionprevnextTop
sub baseat {
    my ($self,$val) = @_;
    return $self->{swq}->subseq($val,$val);
}
subqualdescriptionprevnextTop
sub subqual {
    my ($self,@args) = @_;
    return $self->{swq}->subqual(@args);
}
qualatdescriptionprevnextTop
sub qualat {
    my ($self,$val) = @_;
    return $self->{swq}->qualat($val);
}
sub_peak_indexdescriptionprevnextTop
sub sub_peak_index {
   my ($self,$start,$end) = @_;
   if( $start > $end ){
       $self->throw("in sub_peak_index, start [$start] has to be greater than end [$end]");
   }

   if( $start <= 0 || $end > $self->length ) {
       $self->throw("You have to have start positive and length less than the total length of sequence [$start:$end] Total ".$self->length."");
   }

   # remove one from start, and then length is end-start
$start--; $end--; my @sub_peak_index_array = @{$self->{peak_indices}}[$start..$end]; # return substr $self->seq(), $start, ($end-$start);
return\@ sub_peak_index_array;
}
sub_tracedescriptionprevnextTop
sub sub_trace {
   my ($self,$base_channel,$start,$end) = @_;
   if( $start > $end ){
       $self->throw("in sub_trace, start [$start] has to be greater than end [$end]");
   }

   if( $start <= 0 || $end > $self->trace_length() ) {
       $self->throw("You have to have start positive and length less than the total length of traces [$start:$end] Total ".$self->trace_length."");
   }

   # remove one from start, and then length is end-start
$start--; $end--; my @sub_peak_index_array = @{$self->trace($base_channel)}[$start..$end]; # return substr $self->seq(), $start, ($end-$start);
return\@ sub_peak_index_array;
}
trace_lengthdescriptionprevnextTop
sub trace_length {
    my $self = shift;
     if ( !$self->trace('a') || !$self->trace('t') || !$self->trace('g') || !$self->trace('c') ) {
           $self->warn("One or more of the trace channels are missing. Cannot give you a length.");

     } 
     my $lengtha = scalar(@{$self->trace('a')});
     my $lengtht = scalar(@{$self->trace('t')});
     my $lengthg = scalar(@{$self->trace('g')});
     my $lengthc = scalar(@{$self->trace('c')});
     if (($lengtha == $lengtht) && ($lengtha == $lengthg) && ($lengtha == $lengthc) ) {
          return $lengtha;
     }
     $self->warn("Not all of the trace indices are the same length".
          " Here are their lengths: a: $lengtha t:$lengtht ".
          " g: $lengthg c: $lengthc");
}
sub_trace_objectdescriptionprevnextTop
sub sub_trace_object {
     my ($self,$start,$end) = @_;
          my ($start2,$end2);
        my @subs = @{$self->sub_peak_index($start,$end)};
        $start2 = shift(@subs);
        $end2 =  pop(@subs);
     my $new_object =  Bio::Seq::SequenceTrace->new(
               -swq =>   Bio::Seq::Quality->new(
                             -seq => $self->subseq($start,$end),
                             -qual     =>   $self->subqual($start,$end),
                             -id    =>   $self->id()
                         ),
             -trace_a  => $self->sub_trace('a',$start2,$end2),
             -trace_t  => $self->sub_trace('t',$start2,$end2),
             -trace_g  => $self->sub_trace('g',$start2,$end2),
             -trace_c  => $self->sub_trace('c',$start2,$end2),
             -peak_indices =>   $self->sub_peak_index($start,$end)

        );
     $new_object->set_accuracies();
     $new_object->_reset_peak_indices();
     return $new_object;
}
_synthesize_tracesdescriptionprevnextTop
sub _synthesize_traces {
     my ($self) = shift;
     $self->peak_indices(qw());
#ml     my $version = 2;
# the user should be warned if traces already exist
#
#
#ml ( my $sequence = $self->seq() ) =~ tr/a-z/A-Z/;
#ml my @quals = @{$self->qual()};
#ml my $info;
# build the ramp for the first base.
# a ramp looks like this "1 4 13 29 51 71 80 71 51 29 13 4 1" times the quality score.
# REMEMBER: A C G T
# note to self-> smooth this thing out a bit later
my $ramp_data; @{$ramp_data->{'ramp'}} = qw( 1 4 13 29 51 75 80 75 51 29 13 4 1 ); # the width of the ramp
$ramp_data->{'ramp_width'} = scalar(@{$ramp_data->{'ramp'}}); # how far should the peaks overlap?
$ramp_data->{'ramp_overlap'} = 1; # where should the peaks be located?
$ramp_data->{'peak_at'} = 7; $ramp_data->{'ramp_total_length'} = $self->seq_obj()->length() * $ramp_data->{'ramp_width'} - $self->seq_obj()->length() * $ramp_data->{'ramp_overlap'}; my $pos; my $total_length = $ramp_data->{ramp_total_length}; $self->initialize_traces("0",$total_length+2); # now populate them
my ($current_base,$place_base_at,$peak_quality,$ramp_counter,$current_ramp,$ramp_position); #ml my $sequence_length = $self->length();
my $half_ramp = int($ramp_data->{'ramp_width'}/2);
for ($pos = 0; $pos<$self->length();$pos++) { $current_base = uc $self->seq_obj()->subseq($pos+1,$pos+1); # print("Synthesizing the ramp for $current_base\n");
my $all_bases = "ATGC"; $peak_quality = $self->qual_obj()->qualat($pos+1); # where should the peak for this base be placed? Modeled after a mktrace scf
$place_base_at = ($pos * $ramp_data->{'ramp_width'}) - ($pos * $ramp_data->{'ramp_overlap'}) - $half_ramp + $ramp_data->{'ramp_width'} - 1; # print("Placing this base at this position: $place_base_at\n");
push @{$self->peak_indices()},$place_base_at; $ramp_position = $place_base_at - $half_ramp; if ($current_base =~ "N" ) { $current_base = "A"; } for ($current_ramp = 0; $current_ramp < $ramp_data->{'ramp_width'}; $current_ramp++) { # print("Placing a trace value here: $current_base ".($ramp_position+$current_ramp+1)." ".$peak_quality*$ramp_data->{'ramp'}->[$current_ramp]."\n");
$self->trace_value_at($current_base,$ramp_position+$current_ramp+1,$peak_quality*$ramp_data->{'ramp'}->[$current_ramp]); } $self->peak_index_at($pos+1, $place_base_at+1 ); #ml my $other_bases = $self->_get_other_bases($current_base);
# foreach ( split('',$other_bases) ) {
# push @{$self->{'text'}->{"v3_base_accuracy"}->{$_}},0;
#}
}
}
_dump_tracesdescriptionprevnextTop
sub _dump_traces {
    my ($self) = @_;
    my (@sA,@sT,@sG,@sC);
    print ("Count\ta\tc\tg\tt\n");
     my $length = $self->trace_length();
    for (my $curr=1; $curr <= $length; $curr++) {
     print(($curr-1)."\t".$self->trace_value_at('a',$curr).
                "\t".$self->trace_value_at('c',$curr).
                "\t".$self->trace_value_at('g',$curr).
                "\t".$self->trace_value_at('t',$curr)."\n");
    }
    return;
}
initialize_tracesdescriptionprevnextTop
sub initialize_traces {
     my ($self,$value,$length) = @_;
     foreach (qw(a t g c)) {
          my @temp;
          for (my $count=0; $count<$length; $count++) {
               $temp[$count] = $value;
          }
          $self->trace($_,\@temp);
     }
}
trace_value_atdescriptionprevnextTop
sub trace_value_at {
     my ($self,$channel,$position,$value) = @_;
     if ($value) {
          $self->trace($channel)->[$position] = $value;
     }
     return $self->sub_trace($channel,($position),($position))->[0];
}
_deprecated_get_scf_version_2_base_structuredescriptionprevnextTop
sub _deprecated_get_scf_version_2_base_structure {
          # this sub is deprecated- check inside SeqIO::scf
my $self = shift; my (@structure,$current); my $length = $self->length(); for ($current=1; $current <= $self->length() ; $current++) { my $base_here = $self->seq_obj()->subseq($current,$current); $base_here = lc($base_here); my $probabilities; $probabilities->{$base_here} = $self->qual_obj()->qualat($current); my $other_bases = "atgc"; my $empty = ""; $other_bases =~ s/$base_here/$empty/e; foreach ( split('',$other_bases) ) { $probabilities->{$_} = "0"; } @structure = ( @structure, $self->peak_index_at($current), $probabilities->{'a'}, $probabilities->{'t'}, $probabilities->{'g'}, $probabilities->{'c'} ); } return\@ structure;
}
_deprecated_get_scf_version_3_base_structuredescriptionprevnextTop
sub _deprecated_get_scf_version_3_base_structure {
     my $self = shift;
     my $structure;
     $structure = join('',$self->peak_indices());
     return $structure;
}
accuraciesdescriptionprevnextTop
sub accuracies {
     my ($self,$channel,$value) = @_;
     if ($value) {
          if (ref($value) eq "ARRAY") {
               $self->{accuracies}->{$channel} = $value;
          }
          else {
               my @acc = split(' ',$value);
               $self->{accuracies}->{$channel} =\@ acc;
          }
     }
     return $self->{accuracies}->{$channel};
}
set_accuraciesdescriptionprevnextTop
sub set_accuracies {
     my $self = shift;
     my $count = 0;
     my $length = $self->length();
     for ($count=1; $count <= $length; $count++) {
          my $base_here = $self->seq_obj()->subseq($count,$count);
          my $qual_here = $self->qual_obj()->qualat($count);
          $self->accuracy_at($base_here,$count,$qual_here);
          my $other_bases = $self->_get_other_bases($base_here);
          foreach (split('',$other_bases)) {
               $self->accuracy_at($_,$count,"null");
          }
     }
}
scf_dumpdescriptionprevnextTop
sub scf_dump {
     my $self = shift;
     my $count;
     for ($count=1;$count<=$self->length();$count++) {
          my $base_here = lc($self->seq_obj()->subseq($count,$count));
          print($base_here." ".sprintf("%05d",$self->peak_index_at($count))."\t");
          foreach (sort qw(a c g t)) {
               print(sprintf("%03d",$self->accuracy_at($_,$count))."\t");
          }
          print("\n");
     }
     $self->_dump_traces();
}
_get_other_basesdescriptionprevnextTop
sub _get_other_bases {
     my ($self,$this_base) = @_;
     $this_base = lc($this_base);
     my $all_bases = "atgc";
     my $empty = "";
     $all_bases =~ s/$this_base/$empty/e;
     return $all_bases;
}
accuracy_atdescriptionprevnextTop
sub accuracy_at {
     my ($self,$base,$position,$value) = @_;
     $base = lc($base);
     if ($value) {
          if ($value eq "null") {
               $self->{accuracies}->{$base}->[$position-1] = "0";
          }
          else {
               $self->{accuracies}->{$base}->[$position-1] = $value;
          }
     }
     return $self->{accuracies}->{$base}->[$position-1];
}

1;
}
General documentation
FEEDBACKTop
Mailing ListsTop
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to one
of the Bioperl mailing lists. Your participation is much appreciated.
  bioperl-l@bioperl.org                  - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
Support Top
Please direct usage questions or support issues to the mailing list:
bioperl-l@bioperl.org
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
with code and data examples if at all possible.
Reporting BugsTop
Report bugs to the Bioperl bug tracking system to help us keep track
the bugs and their resolution. Bug reports can be submitted via the
web:
  https://redmine.open-bio.org/projects/bioperl/
AUTHOR - Chad MatsallaTop
Email bioinformatics@dieselwurks.com
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
_initialize_traces()Top
 Title   : _initialize_traces()
Usage : $trace_object->_initialize_traces();
Function: Creates empty arrays to hold synthetic trace values.
Returns : Nothing.
Args : None.